So I am working with ATAC-seq data and wondering if there is a way to extract peaks that are above a certain threshold. For example, I want to extract peaks that are above the red line shown in the picture. Is this something I need to do at the time of peak calling? or can it be done after peak calling?
I am very new to ATAC-seq field so it's difficult to phrase what I am looking for into the right sentence. so please bear with me.
For your information, I just have bed and bigwig files.
If anyone could walk me through how to do that, I would greatly appreciate it!
All the best,